Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1363 to 1412 of 3228 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
network_comparison
green
1363 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] 6322.75 1.07872 6820.5
1364 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] 5815.14 1.07868 6272.66
1365 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] 5799.14 1.07862 6255.04
1366 megf11 protein. [refseq;acc:nm_032445] 5793.55 1.07858 6248.79
1367 megf10 protein. [refseq;acc:nm_032446] 5793.47 6248.71
1368 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 5793.29 6248.51
1369 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 5786.71 1.07853 6241.16
1370 t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] 10231.8 1.07847 9487.34
1371 double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]
1372 lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] 5743.45 1.07835 6193.45
1373 mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] 6079.85 1.07833 6556.07
1374 ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] 6079.45 1.07829 6555.4
1375 calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555]
1376 calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] 6079.46 6555.41
1377 mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] 6555.4
1378 signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 6079.45
1379 ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418] 6079.46 6555.41
1380 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288]
1381 glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947]
1382 histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357]
1383 ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] 6079.45 6555.4
1384 ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [swissprot;acc:q15349]
1385 calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7]
1386 calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] 6079.46 6555.41
1387 mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] 6555.4
1388 lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] 5743.39 1.07827 6192.94
1389 mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482] 6079.13 1.07825 6554.85
1390 receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] 5743.36 1.07824 6192.72
1391 epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] 6192.7
1392 receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626]
1393 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 6192.72
1394 receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860]
1395 lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] 5743.26 1.07813 6191.96
1396 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 5803.54 1.07806 6256.54
1397 heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] 5803.27 1.07805 6256.23
1398 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] 5803.12 6256.05
1399 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] 5803.1 6256.03
1400 heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] 5803.45 6256.43
1401 hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] 5728.92 1.07804 6175.99
1402 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 6160.06 6640.78
1403 importin 4. [refseq;acc:nm_024658] 5613.16 1.07785 6050.16
1404 mesoderm induction early response 1. [refseq;acc:nm_020948] 6291.89 1.07783 6781.6
1405 proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788]
1406 ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] 6210.51 1.07777 6693.49
1407 transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] 5692.53 1.07766 6134.64
1408 serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] 6268.94 1.07763 6755.57
1409 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] 5358.19 1.07749 5773.37
1410 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] 6274.62 1.07748 6760.78
1411 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] 5812.02 1.07743 6262.07
1412 histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] 5813.84 1.07742 6263.92

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/